Detection of chromosomal imbalances in retinoblastoma by matrix‐based comparative genomic hybridization

Abstract

The genetic hallmark of retinoblastoma is mutation or deletion of the RB1 gene, whereas other genetic alterations that are also required are largely unknown. To screen for genomic imbalances on a genomewide level, we studied a series of 17 primary retinoblastomas by matrix-based comparative genomic hybridization (matrix-CGH). The matrix-CGH chip contained 6,000 immobilized genomic DNA fragments covering the human genome, with an average resolution of about 500 kb. The most frequent imbalances detected were gains on chromosome arms 1q (12 of 17), 6p (10 of 17), 2p (5 of 17), and 19q (4 of 17) and loss on 16q (7 of 17). Candidate regions could be narrowed to small intervals by the identified minimally overlapping regions on 1q22, 1q32.1q32.2, 2p24.1, and 6p21.33-p21.31. Furthermore, two as-yet-unknown high-level amplifications were detected, each in a single patient, on chromosome bands 1p34.2 and 1p33. Thus, this study identified new chromosomal regions and therefore potential candidate genes that may play a role in retinoblastoma.

Molecular classification of diffuse cerebral WHO grade II/III gliomas using genome- and transcriptome-wide profiling improves stratification of prognostically distinct patient groups

“…Array assembly, probe labeling, array hybridization and scanning were carried out essentially as reported elsewhere [43]. To identify amplification events, genomic profiles were generated for each tumor and amplifications scored if log 2 test/reference ratios were > 1.…”

Comprehensive genetic and functional characterization of IPH‐926: a novel CDH1‐null tumour cell line from human lobular breast cancer

“…They allow a genome-wide resolution of 1 Mb and an even higher resolution of up to 100 kb for chromosome regions recurrently involved in human tumours. Isolation and spotting of DNA probes were performed as described previously [33]. Probe processing and image analysis were carried out as published earlier [34].…”

Towards mapping phenotypical traits in 18p− syndrome by array-based comparative genomic hybridisation and fluorescent in situ hybridisation

“…Her gross motor skills were delayed by 3 -4 months. She could walk without assistance at the age of 1 10 12 years and speak at the age of 3 years. She had two febrile convulsions at the ages of 2 6 12 and 3 6 12 years.…”

“…Upon clinical examination at 8 3 12 years, she showed muscular hypotonia, ataxia and tetraparesis. At the age of 9 10 12 years, mental retardation was diagnosed by short nonverbal intelligence testing. Electroencephalography showed markedly slow basal activity with sharp-slowwave-complexes confirming epileptic potential despite continuous antiepileptic medication.…”

“…Except for the addition of 2000 region specific clones from the RPCI (RZPD, Berlin, Germany) and CalTech (Invitrogen, Karlsruhe, Germany) BAC libraries, the array has been published previously. 10 Array assembly, hybridisation and analysis were essentially performed as described previously. 10 …”